The warning at the top of the README does the most useful work here: this is for developing Nextflow, and someone arriving to get help writing a pipeline is in the wrong place. For the audience it is aimed at, the value is that build-and-test loops on a large JVM codebase are exactly the commands nobody remembers the flags for, and asking for a plugin's tests in plain language is faster than looking them up.
A FastMCP server for people working on the Nextflow codebase, not for people writing Nextflow pipelines — the README states that distinction up front. It wraps the build, test and run commands of a local Nextflow checkout so an agent can drive them.
- Building Nextflow from source
- Running tests: the integration suite, a specific test, or one plugin's tests — asking to test the nf-amazon plugin runs `make test module=plugins:nf-amazon`
- Running the development version of Nextflow you just built
- Managing the Nextflow development directory
- Access to the Nextflow documentation from the same connection
A local clone of the Nextflow git repository, with its path in `NEXTFLOW_DIR` — that is the one thing without which nothing works. Python 3.8+ with pip, plus the FastMCP CLI (`pip install fastmcp`). For Claude Desktop, `fastmcp install mcp-nextflow.py` registers it, optionally with the directory set on the same command. For Cursor, point the config at your virtual environment's Python and the `mcp-nextflow.py` path with the directory in the env block.